Potentially active rRNA genes exhibit an ‚open’ chromatin structure and are characterized by DNA hypomethylation, and euchromatic histone marks. Epigenetically silenced rRNA genes are demarcated by CpG hypermethylation (CH3), heterochromatic histone marks (Me) and association with heterochromatin protein 1 (HP1). | © dkfz.de

rRNA genes (rDNA) exist in two distinct types of chromatin, an ‘open’ one that is permissive to transcription and a ‘closed’ one that is transcriptionally refractive. The mechanisms that maintain the ratio of active vs. silent rDNA repeats are poorly understood. Our research aims at understanding the principles that establish and propagate the active and silent state of rRNA genes.

We have identified and functionally characterized NoRC (Nucleolar Remodeling Complex), a novel member of SNF2h/ISWI-containing chromatin remodeling complexes. NoRC recruits DNA methyltransferase and histone deacetylases and methyltransferases to the rDNA promoter, thereby triggering heterochromatin formation. NoRC-mediated changes in chromatin structure lead to repression of rDNA transcription and to resetting replication timing from early to late. It seems that NoRC serves at least two functions: first, as a remodeling complex that alters the nucleosome position at the rDNA promoter; and second, as a scaffold that coordinates the activities of macromolecular complexes that modify histones, methylate DNA and establish a ’closed’ heterochromatic chromatin state.

NoRC coordinates rDNA silencing through several epigenetic layers. | © dkfz.de

We found that transcripts originating from the intergenic spacer (IGS) that separate rDNA repeats are required for establishing and maintaining a specific heterochromatic chromatin configuration at a subset of rDNA arrays. The mechanism of action appears to be mediated through interaction of the chromatin remodeling complex NoRC with pRNA, i.e. processed intergenic transcripts that match the rDNA promoter sequence. Knockdown of pRNA abolishes the nucleolar localization of NoRC, decreases DNA methylation and enhances rDNA transcription. The discovery of small regulatory RNA playing a crucial role in the epigenetic control of rDNA extends the importance of noncoding (nc)RNAs as key regulators of gene expression. Recently, we have discovered the presence of antisense (as) transcripts originating from the rDNA locus. Suggesting the potential for dsRNA formation, this leads us into the field of small interfering RNAs. One of our current goals is to investigate this emerging network of regulatory ncRNAs and their role in rDNA silencing.